diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/endpoints.R | 33 | ||||
| -rw-r--r-- | R/saem.R | 4 |
2 files changed, 29 insertions, 8 deletions
diff --git a/R/endpoints.R b/R/endpoints.R index 9ea0e598..0aafd728 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -14,10 +14,11 @@ #' another object that has list components mkinmod containing an [mkinmod] #' degradation model, and two numeric vectors, bparms.optim and bparms.fixed, #' that contain parameter values for that model. -#' @param \dots Possibility to specify values for the covariates in the model. -#' In case more than one vector is given, they either have to be of the same -#' length, or of length one, in which case the respective covariate values are -#' recycled. +#' @param covariates Numeric vector with covariate values for all variables in +#' any covariate models in the object. If given, it overrides 'covariate_quantile'. +#' @param covariate_quantile This argument only has an effect if the fitted +#' object has covariate models. If so, the default is to show endpoints +#' for the median of the covariate values (50th percentile). #' @importFrom stats optimize #' @return A list with a matrix of dissipation times named distimes, and, if #' applicable, a vector of formation fractions named ff and, if the SFORB model @@ -38,14 +39,34 @@ #' } #' #' @export -endpoints <- function(fit, ..., covariates = mean) { +endpoints <- function(fit, covariates = NULL, covariate_quantile = 0.5) { mkinmod <- fit$mkinmod obs_vars <- names(mkinmod$spec) - degparms <- c(fit$bparms.optim, fit$bparms.fixed) + if (!is.null(fit$covariate_models)) { + if (is.null(covariates)) { + covariates = as.data.frame( + apply(fit$covariates, 2, quantile, + covariate_quantile, simplify = FALSE)) + } else { + covariates <- data.frame("User" = covariates) + } + degparms_trans <- parms(fit, covariates = covariates)[, 1] + if (inherits(fit, "saem.mmkin") & (fit$transformations == "saemix")) { + degparms <- degparms_trans + } else { + degparms <- backtransform_odeparms(degparms_trans, + fit$mkinmod, + transform_rates = fit$transform_rates, + transform_fractions = fit$transform_fractions) + } + } else { + degparms <- c(fit$bparms.optim, fit$bparms.fixed) + } # Set up object to return ep <- list() + ep$covariates <- covariates ep$ff <- vector() ep$SFORB <- vector() ep$distimes <- data.frame( @@ -802,14 +802,14 @@ update.saem.mmkin <- function(object, ..., evaluate = TRUE) { } #' @export -#' @rdname saem +#' @rdname parms #' @param ci Should a matrix with estimates and confidence interval boundaries #' be returned? If FALSE (default), a vector of estimates is returned if no #' covariates are given, otherwise a matrix of estimates is returned, with #' each column corresponding to a row of the data frame holding the covariates #' @param covariates A data frame holding covariate values for which to #' return parameter values. Only has an effect if 'ci' is FALSE. -parms.saem.mmkin <- function(object, ci = FALSE, covariates = NULL, covariate_quantiles = ...) { +parms.saem.mmkin <- function(object, ci = FALSE, covariates = NULL, ...) { cov.mod <- object$sm@covariance.model n_cov_mod_parms <- sum(cov.mod[upper.tri(cov.mod, diag = TRUE)]) n_parms <- length(object$sm@name.modpar) + |